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PubMed1998

The telemedicine information exchange: an online resource.

Telemedicine is the use of telecommunications to provide health care services at a distance. It has grown from mostly government-subsidized research initiatives into a fledgling industry. This growth was fueled by decreasing costs of telecommunications and information technologies and fanned by rising health care costs. The telemedicine information exchange (TIE) (http:(/)/tie.telemed.org), developed by the Telemedicine Research Center in Portland, OR, is both a product and a vehicle of this rapid growth. It facilitates collection of telemedicine information from many sources, providing an easy-to-use hypertext format. This article describes the TIE's development, advantages and disadvantages of a web-based online library, and it's codevelopment with a rapidly expanding industry.

Costs and Cost Analysis↗
PubMed1994

Using focus groups to discover health professionals' information needs: a regional marketing study.

This paper describes the use of focus groups as a data-gathering tool, in both theoretical and practical terms. Calder's discussion of focus groups is presented as the basis of the theory, and the marketing study conducted by the Midcontinental Region of the National Network of Libraries of Medicine serves as the backdrop to highlight some of the practical aspects of using this qualitative data-gathering method. Results of the marketing study are presented to illustrate the types of data that can be gathered using this methodology and the types of plans for future activities that can be developed based on the data gathered.

Communication↗
PubMed1982

International exchange of scientific literature by U.S. academic health sciences libraries: a literature review and survey of current activities.

This paper reports results of a literature review and survey of current international exchange activities in 124 academic health sciences libraries in the United States. It describes the extent to which those libraries engage in exchange programs, the kinds of material sent and received, and the common problems in establishing and maintaining exchange relationships. Preferences of the respondents for future exchange programs are identified and recommendations for enhancing their value are made. The work reported is being used by the Medical Library Association Ad Hoc Committee on the International Exchange and Redistribution of Library Materials to develop a more workable and effective mechanism for continuing the international exchange of scientific literature and for facilitating the dissemination of scientific information to national and international network users.

Academic Medical Centers↗
PubMed1995

[IMAGE: molecular integration of the analysis of the human genome and its expression].

We have developed an integrated approach for the analysis of human cDNA libraries from neuromuscular tissues, based on the acquisition of primary structural, expression and mapping data. 26,938 sequence signatures (over 7 million bases) have been derived from both ends of skeletal muscle and brain cDNA clones. Primary redundancy analysis and classification of database similarities made it possible to characterize by structural data about 8,000 human gene transcripts, the majority of which is catalogued for the first time. Collecting hybridization signatures of complex cDNA probes derived from the tissues of origin to cDNA clones arrayed on high density filters provided a global and quantifiable view of the complexity and level of expression of the different transcripts. The development of 2,792 eSTS markers amplifiable by PCR defined the chromosomal localization of some 2,500 genes corresponding to the transcripts sequenced. The data collected are part of the corpus of the human gene transcript catalog and the genic map of the human genome.

Brain Chemistry↗
PubMed1986

The patient-centered bibliography: uniting library services with the mission of the psychiatric hospital.

The primary function of a hospital is patient care. The development of a patient-centered bibliography is suggested as the most effective way of organizing information and insuring its use in the psychiatric hospital. The patient-centered bibliography is a collection of readings which are especially pertinent to the care of an individual patient. It consists of a core of current literature organized around the patient's multiaxial diagnosis (including psychosocial stresses), but may also include articles on psychopharmacology, special psychotherapeutic techniques, and literature on family dynamics. The collection can be expanded to include patient-centered information for two other purposes as well: milieu therapy and patient education.

Bibliographies as Topic↗
PubMed2006

Health sciences librarians' reference services during a disaster: more than collection protection.

Reliable and timely professional information services are always important, but even more so during a community-wide disaster, like the aftermath of Hurricane Katrina. There are classes and literature on planning for library collection protection in local emergencies, but little about planning for reference and information services. Four accounts from South Louisiana in September of 2005 demonstrate the value of proactive and innovative services based on professional information needs analysis skills. More study of such cases could lead to the development of best practice guidelines for the planning and provision of disaster information services.

Disasters↗
PubMed1998

Derivatization procedures for gas chromatographic-mass spectrometric determination of xenobiotics in biological samples, with special attention to drugs of abuse and doping agents.

The development of low cost MS detectors in recent years has promoted an important increase in the applicability of GC-MS system to analyze for the presence of foreign substances in the human body. Drugs and toxic agents are in vivo metabolized in such a way that more polar compounds are usually formed. Derivatization of these metabolites is often an unavoidable requirement for gas chromatographic analysis. Application of derivatization methods in recent years has been relevant, especially for silylation, acylation, alkylation and the formation of cyclic or diastereomeric derivatives. Given the relevance of drug of abuse testing in modern toxicology, main derivatization procedures for opiates, cocaine, cannabis, amphetamines, benzodiazepines and LSD have been reviewed. Papers describing the analyses of drugs of abuse in matrixes other than blood, such as hair or sweat, have received special attention. Advances in derivatization for sports drug testing have been particularly relevant for anabolic steroids, diuretics and corticosteroids. Among the several methodologies applied, the formation of trimethylsilyl, perfluoroacyl or methylated derivatives have proved to be both versatile and extensively used. Further advances in derivatization for GC-MS applications in clinical and forensic toxicology will depend on the one hand on the degree of further use of GC-MS for routine applications and, on the other hand, on the alternative progress made for developments in LC-MS or CE-MS. Last but not least, the appearance of comprehensive libraries in which reference spectra for different derivatives of many drugs and their metabolites are collected will have an important impact on the expansion of derivatization in GC-MS for toxicological applications.

Body Fluids↗
PubMed2000

Analysis of libraries encoded with GC tags: compound elution, tag decode analysis, and statistical sampling analysis.

Libraries encoded with electrophoric tags present a unique challenge with respect to library quality control and characterization. Libraries are prepared on Tentagel resin in 200-fold redundancy wherein each resin particle contains one compound per one tag set. The amount of compound present on the bead is ca. 200-500 pmole while tag levels are estimated at 0.5-1 pmol/bead. Several quality control protocols have been developed in order to accurately estimate bead yield and purity for the entire library, ensure high tag fidelity, and to determine the overall performance of individual synthons. This review provides a unique, collective portrait of Pharmacopeia's approach in assessing the quality of libraries prepared using its molecular encoding technology.

Chromatography, Liquid↗
PubMed2006

A high-throughput method for cloning and sequencing human immunodeficiency virus type 1 integration sites.

Integration of retroviral DNA is nonspecific and can occur at many sites throughout chromosomes. However, the process is not uniformly distributed, and both hot and cold spots for integration exist. The mechanism that determines target site specificity is not well understood. Because of the nonspecific and widespread nature of integration, studies analyzing the mechanism and factors that control target site selection require the collection and analysis of a large library of human immunodeficiency virus type 1 (HIV-1) proviral clones. Such analyses are time-consuming and labor-intensive using conventional means. We have developed an efficient and high-throughput method of sequencing and mapping a large number of independent integration sites in the absence of any selection or bias. The new assay involves the use of a modified HIV-1 (NL-Mme) containing a type IIS restriction site, MmeI, at the right end of viral DNA. Digestion of genomic DNA from NL-Mme-infected cells generated viral DNA-containing fragments of a discrete size. Subsequent ligation-mediated PCR yielded short integration site fragments termed Int-tags, which were concatemerized for determining multiple integration sites in a single sequencing reaction. Analysis of chromosomal features and sequence preference associated with integration events confirmed the validity of the new high-throughput assay. The assay will aid the effort in understanding the mechanisms of target site selection during HIV-1 DNA integration, and the described methodology can be adapted easily to integration site studies involving other retroviruses and transposons.

Cell Line↗
PubMed2004

Deriving knowledge through data mining high-throughput screening data.

Deriving general knowledge from high-throughput screening data is made difficult by the significant amount of noise, arising primarily from false positives, in the data. The paradigm established for screening an encoded combinatorial library on polymeric support, an ECLiPS library, has a significant amount of built-in redundancy. Because of this redundancy, the resulting data can be interpreted through a rigorous statistical analysis procedure, thereby significantly reducing the number of false positives. Here, we develop the statistical models used to analyze data from high-throughput screens of ECLiPS libraries to derive unbiased true hit rates. These hit rates can also be calculated on subsets of the collection such as those compounds containing a carboxylic acid or those with molecular weight below 350 Da. The relative value of the hit rate on the subset of the collection can then be compared to the overall hit rate to determine the effect of the substructure or physical property on the likelihood of a molecule having biological activity. Here, we show the effects that various functional groups and the standard physical properties, molecular weight, hydrogen bond donors, hydrogen bond acceptors, log P, and rotatable bonds, have on the likelihood of a compound being biologically active. To our knowledge this is the first published account of the use of high-throughput screening data to elucidate the effects of physical properties and substructures on the likelihood of compounds showing biological activity over a broad range of pharmaceutically relevant targets.

Algorithms↗
PubMed2006

Discovery of trypanocidal compounds by whole cell HTS of Trypanosoma brucei.

Chemotherapy against human African trypanosomiasis relies on four drugs that cause frequent and occasionally severe side-effects. Because human African trypanosomiasis is a disease of poor people in Africa, the traditional market-driven pathways to drug development are not available. One potentially rapid and cost-effective approach to identifying and developing new trypanocidal drugs would be high throughput-screening of existing drugs already approved for other uses, as well as clinical candidates in late development. We have developed an ATP-bioluminescence assay that could be used to rapidly and efficiently screen compound libraries against trypanosomes in a high throughput-screening format to validate this notion. We screened a collection of 2160 FDA-approved drugs, bioactive compounds and natural products to identify hits that were cytotoxic to cultured Trypanosoma brucei at a concentration of 1 mum or less. This meant that any hit identified would be effective at a concentration readily achievable by standard drug dosing in humans. From the screen, 35 hits from seven different drug categories were identified. These included the two approved trypanocidal drugs, suramin and pentamidine, several other drugs suspected but never validated as trypanocidal, and 17 novel trypanocidal drugs.

Animals↗
PubMed1993

Appropriate information: new products and services.

Effective health information services require action on three major levels: identifying and acquiring appropriate resources; applying appropriate methodologies for management of information and its communication; and stimulating local initiatives and applications. WHO's Programme of Library and Health Literature Services proposes its methodologies and products for creating and improving effective information services to health workers.

Developing Countries↗
PubMed2001

Structured data management--the design and implementation of a web-based video archive prototype.

In response to the lack of readily available multimedia rich medical knowledge sources to support medical education and patient care, we designed and implemented a web-based video publishing platform. In order to promote the development of high-quality, up-to-date educational content, we have devised a scalable structure that allows online submissions and continuous updating of video and accompanying textual descriptions. Our goal is to enable experts in varied medical domains to collaborate in the construction of a video library using an intuitive web-based interface. Neurologists at Stanford built a well-annotated neurology video collection that initially emphasized childhood and adult movement disorders. The collection may be accessed either as a stand-alone resource or as part of the Stanford Skolar MD, an integrated online medical knowledge provider. This manuscript discusses the design framework and implementation details of structured media content development. We present examples illustrating media data collection, content indexing using UMLS concepts, media storage, and web presentation.

Abstracting and Indexing↗
PubMed1999

Improving usage of pediatric information on the Internet: the Virtual Children's Hospital.

OBJECTIVE: Digital health sciences libraries (DHSLs) bring order to the chaos of the Internet by making authoritative medical information easily and conveniently available to patrons. The goal of this project was to perform a baseline usage analysis of the pediatric-related information in a general DHSL and to determine whether reorganization of the pediatric-related information into its own pediatric DHSL could increase the usage of the pediatric-related information. METHODS: From March through August 1997, a baseline analysis of a general DHSL (Virtual Hospital) was conducted using computer server log file analysis programs. The quantity of pediatric-related information in the general DHSL and its baseline usage were determined. In September 1997, the pediatric-related information was reorganized into its own pediatric DHSL (Virtual Children's Hospital), and server log file analyses were conducted of the pediatric DHSL from September 1997 to August 1998. Statistical analysis was performed by time series autoregression. RESULTS: During the baseline, the general DHSL and the pediatric-related information received a monthly average of 2 320 782 and 141 444 qualified hits, respectively. After the intervention, the general DHSL and the pediatric DHSL received a monthly average of 2 765 454 and 256 998 qualified hits, respectively. This is an increase of 19. 2% for the general DHSL and 81.7% for the pediatric DHSL. These changes were statistically significant at the P >.0001 level. The most requested pediatric-related content in the pediatric DHSL did not change substantively from preintervention to postintervention. DISCUSSION: On the Internet, as in real life, children's services must have their own distinct identity and must be differentiated from adult services. Therefore, pediatric-related information will receive increased usage if it is part of a pediatric DHSL rather than part of a general DHSL. Others can use this process and the lessons learned to develop and enhance their own pediatric-related information on the Internet. Internet, pediatrics, digital health sciences libraries, digital library, medical library.

Data Collection↗
PubMed1997

Using the Internet as a teaching strategy: informatics at work.

Development of the World Wide provides educators with an enormous library of teaching tools. The purpose of this presentation is to share the results of introducing over 60 graduate students to use e-mail, internet mailing lists, computer conferences, and the World Wide Web as teaching strategies. Data were collected from students through questions and Electronic Communication Logs. Response of the students was categorized into 6 phases: 1) fear and trepidation, 2) excitement, "this is great!", 3) "help, my mail box is full", 4) venturing forth independently, 5) this is easy, and 6) accepting the internet as a useful tool. Identification of these phases provided a basis for developing teaching strategies specific to internet uses. Feedback between students and instructor increased and was far more timely than occurs in the classroom setting. The student responses to these experiences were overwhelmingly positive.

Computer Communication Networks↗
PubMed2007

Creation of a CT Image Library for the Lung Screening Study of the National Lung Screening Trial.

The CT Image Library (CTIL) of the Lung Screening Study (LSS) network of the National Lung Screening Trial (NLST) consists of up to three annual screens using CT imaging from each of 17,308 participants with a significant history of smoking but no evidence of cancer at trial enrollment (Fall 2002-Spring 2004). Screens performed at numerous medical centers associated with 10 LSS-NLST screening centers are deidentified of protected health information and delivered to the CTIL via DVD, external hard disk, or Internet/Virtual Private Network transmission. The collection will be completed in late 2006. The CTIL is of potential interest to clinical researchers and software developers of nodule detection algorithms. Its attractiveness lies in its very specific, well-defined patient population, scanned via a common CT protocol, and in its collection of evenly spaced serial screens. In this work, we describe the technical details of the CTIL collection process from screening center retrieval through library storage.

Clinical Protocols↗
PubMed2005

In pursuit of effective toxicogenomics.

Biological systems exhibit complex responses to xenobiotics varying from generic stress responses to very specific changes closely associated with the mechanism of toxicity. Until recently our view of this complexity was obscured by the simplicity of available analysis tools which allowed determination of only a few genes in any one study. Then genome sequencing and high throughput library screening projects delivered data on the genome sequence of many organisms, and clones were collected and made available to researchers in a previously unparalleled quantity. To exploit this new resource the microarray was developed from its predecessor the dot blot. Further development has expanded the number of clones contained on any one microarray to a point where the expression of many tens of thousands of genes in a biological system can be determined in a short period of time. What these data are revealing is the full complexity of the gene expression response to stimuli such as xenobiotic exposure. Toxicogenomics seeks to use the complexity of this response as a fingerprint or signature characteristic of that xenobiotic exposure. There are though two major experimental challenges that need to be dealt with for toxicogenomics to be successful. The first is technical and relates to the intrinsic difficulties associated with the accurate measurement of gene expression. For microarrays, this problem is multiplied by the number of genes on the microarray itself. To overcome this technical variability correct experimental design is critical. The second challenge concerns the biological system used. What genetic background, time point and dose of xenobiotic should be chosen? For in vitro systems should cell lines or primary cells be used? These factors, and more, could affect the gene expression profile obtained in response to the same xenobiotic exposure. Using both our data and data from public databases these issues are explored in this paper.

Animals↗
PubMed1998

A genetic algorithm for designing gene family-specific oligonucleotide sets used for hybridization: the G protein-coupled receptor protein superfamily.

MOTIVATION: Massive oligonucleotide hybridization is one of the most promising technologies of functional genome analysis. The critical point is to design appropriate sets of oligonucleotides that can be used effectively in identification by hybridization. RESULTS: Using a genetic algorithm approach, we have attempted to design sets of oligo probes capable of identifying new genes belonging to a defined gene family within a cDNA or genomic library. It is not limited by oligonucleotide length and admits the letter 'N' in the structure of the oligonucleotides selected. One of the major advantages of this approach is the low homology required to identify functional families of sequences with little homology. We have designed the oligonucleotide sets that are most selective for the cDNA clones of transmembrane G protein-coupled receptors (GPCRs), a large family of proteins that form part of a modular system of extracellular signal transduction to the intracellular second messenger pathways. The accuracy of identification has been checked on the EST library containing 713 870 cDNA sequences. A set of 15 oligos between 7 and 14 bases in length has correctly identified 70% of the GPCR cDNA collection sequences with 0.02% false positives. AVAILABILITY: The developed software is available by ftp://ftp.bionet.nsc. ru/pub/biology/ and on the Web page http://www.bionet.nsc. ru/SRCG/Oligoselector/. CONTACT: kel@.bionet.nsc.ru; sebastian. meier-ewert@gpc-ag.com

Algorithms↗